BLASTBLASTThe Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

http://www.ncbi.nlm.nih.gov/blast

Nucleotide BLASTNucleotide BLAST

Protein BLASTProtein BLAST

>gi|114520617|ref|NM_021130.3| Homo sapiens peptidylprolyl isomerase A (cyclophilin A) (PPIA), mRNA GAACGTGGTATAAAAGGGGCGGGAGGCCAGGCTCGTGCCGTTTTGCAGACGCCACCGCCGAGGAAAACCG TGTACTATTAGCCATGGTCAACCCCACCGTGTTCTTCGACATTGCCGTCGACGGCGAGCCCTTGGGCCGC GTCTCCTTTGAGCTGTTTGCAGACAAGGTCCCAAAGACAGCAGAAAATTTTCGTGCTCTGAGCACTGGAG AGAAAGGATTTGGTTATAAGGGTTCCTGCTTTCACAGAATTATTCCAGGGTTTATGTGTCAGGGTGGTGA CTTCACACGCCATAATGGCACTGGTGGCAAGTCCATCTATGGGGAGAAATTTGAAGATGAGAACTTCATC CTAAAGCATACGGGTCCTGGCATCTTGTCCATGGCAAATGCTGGACCCAACACAAATGGTTCCCAGTTTT TCATCTGCACTGCCAAGACTGAGTGGTTGGATGGCAAGCATGTGGTGTTTGGCAAAGTGAAAGAAGGCAT GAATATTGTGGAGGCCATGGAGCGCTTTGGGTCCAGGAATGGCAAGACCAGCAAGAAGATCACCATTGCT GACTGTGGACAACTCGAATAAGTTTGACTTGTGTTTTATCTTAACCACCAGATCATTCCTTCTGTAGCTC AGGAGAGCACCCCTCCACCCCATTTGCTCGCAGTATCCTAGAATCTTTGTGCTCTCGCTGCAGTTCCCTT TGGGTTCCATGTTTTCCTTGTTCCCTCCCATGCCTAGCTGGATTGCAGAGTTAAGTTTATGATTATGAAA TAAAAACTAAATAACAATTGTCCTCGTTTGAGTTAAGAGTGTTGATGTAGGCTTTATTTTAAGCAGTAAT GGGTTACTTCTGAAACATCACTTGTTTGCTTAATTCTACACAGTACTTAGATTTTTTTTACTTTCCAGTC CCAGGAAGTGTCAATGTTTGTTGAGTGGAATATTGAAAATGTAGGCAGCAACTGGGCATGGTGGCTCACT GTCTGTAATGTATTACCTGAGGCAGAAGACCACCTGAGGGTAGGAGTCAAGATCAGCCTGGGCAACATAG TGAGACGCTGTCTCTACAAAAAATAATTAGCCTGGCCTGGTGGTGCATGCCTAGTCCTAGCTGATCTGGA GGCTGACGTGGGAGGATTGCTTGAGCCTAGAGTGAGCTATTATCATGCCACTGTACAGCCTGGGTGTTCA CAGATCTTGTGTCTCAAAGGTAGGCAGAGGCAGGAAAAGCAAGGAGCCAGAATTAAGAGGTTGGGTCAGT CTGCAGTGAGTTCATGCATTTAGAGGTGTTCTTCAAGATGACTAATGTCAAAAATTGAGACATCTGTTGC GGTTTTTTTTTTTTTTTTTTCCCCTGGAATGCAGTGGCGTGATCTCAGCTCACTGCAGCCTCCGCCTCCT GGGTTCAAGTGATTCTAGTGCCTCAGCCTCCTGAGTAGCTGGGATAATGGGCGTGTGCCACCATGCCCAG CTAATTTTTGTATTTTTAGTATAGATGGGGTTTCATCATTTTGACCAGGCTGGTCTCAAACTCTTGACCT CAGCTGATGCGCCTGCCTTGGCCTCCCAAACTGCTGAGATTACAGATGTGAGCCACCGCACCCTACCTCA TTTTCTGTAACAAAGCTAAGCTTGAACACTGTTGATGTTCTTGAGGGAAGCATATTGGGCTTTAGGCTGT AGGTCAAGTTTATACATCTTAATTATGGTGGAATTCCTATGTAGAGTCTAAAAAGCCAGGTACTTGGTGC TACAGTCAGTCTCCCTGCAGAGGGTTAAGGCGCAGACTACCTGCAGTGAGGAGGTACTGCTTGTAGCATA TAGAGCCTCTCCCTAGCTTTGGTTATGGAGGCTTTGAGGTTTTGCAAACCTGACCAATTTAAGCCATAAG ATCTGGTCAAAGGGATACCCTTCCCACTAAGGACTTGGTTTCTCAGGAAATTATATGTACAGTGCTTGCT GGCAGTTAGATGTCAGGACAATCTAAGCTGAGAAAACCCCTTCTCTGCCCACCTTAACAGACCTCTAGGG TTCTTAACCCAGCAATCAAGTTTGCCTATCCTAGAGGTGGCGGATTTGATCATTTGGTGTGTTGGGCAAT TTTTGTTTTACTGTCTGGTTCCTTCTGCGTGAATTACCACCACCACCACTTGTGCATCTCAGTCTTGTGT GTTGTCTGGTTACGTATTCCCTGGGTGATACCATTCAATGTCTTAATGTACTTGTGGCTCAGACCTGAGT GCAAGGTGGAAATAAACATCAAACATCTTTTCATTA

http://www.ncbi.nlm.nih.gov/

blast-2.2.18-ia32-win32.exe

netblast-2.2.18-ia32-win32.exe

DOWNLOAD:

netblast-2.2.18-ia32-win32.exe Blast NCBI Database

Create a folder “NETBLAST” in “C” DriveDownload netblast-2.2.18-ia32-win32.exeDecompress the file

COMMAND開始執行 cmd

cd/cd\NETBLAST\blastcl3 -p blastn -i c:\NETBLAST\FILENAME -d nr -o c:\NETBLAST\FILENAME-BLASTn_-nr.txt

-p program-I input file-d database-o output file

OPTIONS:-m 8 tubular output-b 1 list one description -v 1 show one alignment

EXERCISE:Use the sequence file from last week’s homework to do a netblast WITH & WITHOUT options

blast-2.2.18-ia32-win32.exe Blast Local Database

Create a folder “NETBLAST” in “C” DriveDownload blast-2.2.18-ia32-win32.exeDecompress the file

COMMAND開始執行 cmdcd/cd\BLAST\bin

CREATE LOCAL DATABSEformatdb -p T -o T -i c:\BLAST\FILENAME (protein)formatdb -p F -o T -i c:\BLAST\FILENAME (nucleotide)

LOCAL BLASTblastall -p blastp -i c:\BLAST\FILENAME -d c:\BLAST\DATABASE -o c:\BLAST\BLASTx-FILENAME.txt

-p program-I input file-d database-o output file

OPTIONS:-m 8 tubular output-b 1 list one description -v 1 show one alignment

EXERCISE:Reformat the sequence file from last week’s homework as a local database.Use the same sequence to do a blast WITH & WITHOUT options